AMBER Archive (2002)

Subject: Re: MM-GBSA and counterions

From: David A. Case (case_at_scripps.edu)
Date: Thu Oct 03 2002 - 15:43:35 CDT

On Thu, Oct 03, 2002, Michael Ford wrote:
>
>
> I was just wondering about thoughts anyone might have as to whether
> counterions neutralizing a ligand charge should be included with
> receptor or ligand in MM-PBSA type calculations. I have a negatively
> charged ligand, neutralized with a sodium counterion. I'm guessing I
> should throw it in with the receptor.

I generally recommend that mobile counterions be treated as a part of the
solvent: they are thrown away before the MM-PBSA calculations start.
Use the "saltcon" variable (for GB) or equivalent in your PB program to
include salt-dependent effects.

[Aside: note that if you use Delphi, you need to take care in doing PB
calculations with non-zero salt: the program's output can be confusing.]

..hope this helps...dac 

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